S. Burkhardt and J. Kärkkäinen, Better Filtering with Gapped q-Grams, Fundamenta Informaticae, vol.56, issue.12, pp.51-70, 2003.
DOI : 10.1007/3-540-48194-X_6

D. Gusfield, G. Landau, and B. Schieber, An efficient algorithm for the All Pairs Suffix-Prefix Problem, Information Processing Letters, vol.41, issue.4, pp.181-185, 1992.
DOI : 10.1016/0020-0190(92)90176-V

J. Kärkkäinen and J. C. Na, Faster Filters for Approximate String Matching, Proc. 9th Workshop on Algorithm Engineering and Experiments (ALENEX), pp.84-90, 2007.
DOI : 10.1137/1.9781611972870.8

G. Kucherov, K. Salikhov, and D. Tsur, Approximate string matching using a bidirectional index, Proceedings of the 25th Annual Symposium on Combinatorial Pattern Matching (CPM), pp.222-231, 1310.
DOI : 10.1016/j.tcs.2015.10.043

URL : https://hal.archives-ouvertes.fr/hal-01086206

T. W. Lam, R. Li, A. Tam, S. C. Wong, E. Wu et al., High Throughput Short Read Alignment via Bi-directional BWT, 2009 IEEE International Conference on Bioinformatics and Biomedicine, pp.31-36, 2009.
DOI : 10.1109/BIBM.2009.42

Z. Li, Y. Chen, D. Mu, J. Yuan, Y. Shi et al., Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph, Briefings in Functional Genomics, vol.11, issue.1, pp.25-37, 2012.
DOI : 10.1093/bfgp/elr035

B. Ma, J. Tromp, and M. Li, PatternHunter: faster and more sensitive homology search, Bioinformatics, vol.18, issue.3, pp.440-445, 2002.
DOI : 10.1093/bioinformatics/18.3.440

E. W. Myers, G. G. Sutton, A. L. Delcher, I. M. Dew, D. P. Fasulo et al., A Whole-Genome Assembly of Drosophila, Science, vol.287, issue.5461, pp.2872196-2204, 2000.
DOI : 10.1126/science.287.5461.2196

G. Navarro and M. Raffinot, Flexible Pattern Matching in Strings ? Practical on-line search algorithms for texts and biological sequences, 2002.

L. Noé and G. Kucherov, YASS: enhancing the sensitivity of DNA similarity search, Nucleic Acids Research, vol.33, issue.Web Server, pp.540-543, 2005.
DOI : 10.1093/nar/gki478

E. Ohlebusch and S. Gog, Efficient algorithms for the all-pairs suffix-prefix problem and the all-pairs substring-prefix problem, Information Processing Letters, vol.110, issue.3, pp.123-128, 2010.
DOI : 10.1016/j.ipl.2009.10.015

J. T. Simpson and R. Durbin, Efficient de novo assembly of large genomes using compressed data structures, Genome Research, vol.22, issue.3, pp.549-556, 2012.
DOI : 10.1101/gr.126953.111

N. Välimäki, S. Ladra, and V. Mäkinen, Approximate all-pairs suffix/prefix overlaps, Information and Computation, vol.213, pp.49-58, 2012.
DOI : 10.1016/j.ic.2012.02.002

M. Vyverman, B. De-baets, V. Fack, and P. Dawyndt, Prospects and limitations of full-text index structures in genome analysis, Nucleic Acids Research, vol.40, issue.15, pp.6993-7015, 2012.
DOI : 10.1093/nar/gks408